X-26637619-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000674719.1(VENTXP1):n.622+75020C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 111,473 control chromosomes in the GnomAD database, including 773 homozygotes. There are 3,802 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (773 hom., 3802 hem., cov: 23)
• Consequence: VENTXP1 ENST00000674719.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

Genes affected

VENTXP1 (HGNC:30900): (VENT homeobox pseudogene 1) Homeobox genes encode DNA-binding proteins, many of which are thought to be involved in early embryonic development. Homeobox genes encode a DNA-binding domain of 60 to 63 amino acids referred to as the homeodomain. This pseudogene is a member of the Vent homeobox gene family. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VENTXP1	ENST00000674719.1	n.622+75020C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.108 AC: 12043 AN: 111424 Hom.: 773 Cov.: 23 AF XY: 0.113 AC XY: 3789 AN XY: 33668

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.0352

Gnomad MID AF: 0.0975

Gnomad NFE AF: 0.0660

Gnomad OTH AF: 0.135

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 12048 AN: 111473 Hom.: 773 Cov.: 23 AF XY: 0.113 AC XY: 3802 AN XY: 33727

Gnomad4 AFR AF: 0.0804

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.0352

Gnomad4 NFE AF: 0.0660

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0832 Hom.: 3012

Bravo AF: 0.133

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.67
Dann	Benign	0.38

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1558145; hg19: chrX-26655736;